pipelines.chromake.scripts.paths

pipelines.chromake.scripts.paths

The paths module of chromake contains functions to identify the inputs and the files generated by the chromake pipeline.

Functions

Name Description
get_all_sequencings_related_paths Get the path to the files generated by the pipeline for the samples of all sequencings and projects.
get_project_paths_for_macs3 Get a dictionary with the files necessary for the macs3 rules of a project.
get_sequencings_related_paths Get the path to the files generated by the pipeline for the samples of a specific sequencing.

get_project_paths_for_macs3

pipelines.chromake.scripts.paths.get_project_paths_for_macs3(
    cfg,
    project_name,
    mode,
)

Get a dictionary with the files necessary for the macs3 rules of a project.

Parameters

Name Type Description Default
cfg dict Dict representing the configuration of an analysis with the chromake pipeline. required
project_name str String representing the name of the project in cfg required
mode str String indicating the output. Accepted values are: - macs3 (dict with all inputs and the outputs of the macs3 command for all samples associated with the project) - macs3_output (list of all outputs of the macs3 command for the project) required

Returns

Name Type Description
A dictionary of all file paths for the project.